Large-scale hydrological modeling is an emerging approach in river hydrology, especially in regions with limited available data. This research focuses on evaluating the performance of two well-known large-scale hydrological models, namely E-HYPE and LISFLOOD, for the five transboundary rivers of Greece. For this purpose, discharge time series at the rivers’ outlets from both models are compared with observed datasets wherever possible. The comparison is conducted using well-established statistical measures, namely, coefficient of determination, Percent Bias, Nash–Sutcliffe Efficiency, Root-Mean-Square Error, and Kling–Gupta Efficiency. Subsequently, the hydrological models’ time series are bias corrected through scaling factor, linear regression, delta change, and quantile mapping methods, respectively. The outputs are then re-evaluated against observations using the same statistical measures. The results demonstrate that neither of the large-scale hydrological models consistently outperformed the other, as one model performed better in some of the basins while the other excelled in the remaining cases. The bias-correction process identifies linear regression and quantile mapping as the most suitable methods for the case study basins. Additionally, the research assesses the influence of upstream waters on the rivers’ water budget. The research highlights the significance of large-scale models in transboundary hydrology, presents a methodological approach for their applicability in any river basin on a global scale, and underscores the usefulness of the outputs in cooperative management of international waters.